0.032374 0.018691 0.000000 0.000000 0.037382 0.000000 0.000000 0.000000 0.008767 0.00000 0.00000 0.00000 3.54356 2.42580 25.62398 1.50364 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 0.51345 0.48472 24.73122 6.32584 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 8.66788 8.58341 1.68052 12.31593 0.56275 110.00227 0.0 3-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 4.01032 2.96436 19.97189 1.75589 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 4.49882 3.47563 15.80542 1.70748 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.51135 5.44231 1.42069 35.72801 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 32.18652 5.63919 2.35430 57.90393 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 0009-0005-1724-9544 Hendrickson, A.D. 0000-0002-5248-142X Xing, E.R. 0000-0003-3946-0939 Yatsunyk, L.A. 0000-0003-3043-8401 Mergny, J.L. 0009-0006-2247-6458 Chen, Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.000 90.000 120.000 30.889 30.889 114.068 94254.513 C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer K 1 39.098 POTASSIUM ION non-polymer C6 H14 O4 150.173 TRIETHYLENE GLYCOL non-polymer Sr 2 87.620 STRONTIUM ION non-polymer N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C N 17 N C N 18 N O N 19 N N N 20 N C N 21 N N N 22 N N Y 23 N C N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 N C N 49 R C N 50 N N N 51 N C N 52 N O N 53 N N N 54 N C N 55 N O N 56 N C N 57 N C N 58 N C N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N O N 75 N H N 76 N H N 77 N K N 78 N C N 79 N O N 80 N C N 81 N O N 82 N C N 83 N C N 84 N O N 85 N C N 86 N C N 87 N O N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N SR N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing N 29 N sing Y 30 N doub N 31 N doub N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N doub N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N doub N 66 N sing N 67 N sing N 68 N sing N 69 N doub N 70 N sing N 71 N sing N 72 N doub N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing To Be Published 0353 SubG4s: A Novel Class of Bulge-Rich G-Quadruplexes 0009-0005-1724-9544 0000-0002-5248-142X 0009-0006-2247-6458 0000-0003-3946-0939 0000-0003-3043-8401 10.2210/pdb9plc/pdb pdb_00009plc 196 Liquid nitrogen 1 N PIXEL 2025-04-30 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 0.979330 1.0 24-ID-E APS 0.979330 SYNCHROTRON APS BEAMLINE 24-ID-E 4109.652 DNA (13-MER) 1 syn polymer 150.173 TRIETHYLENE GLYCOL 1 syn non-polymer 39.098 POTASSIUM ION 2 syn non-polymer 87.620 STRONTIUM ION 2 syn non-polymer 18.015 water 5 nat water no no (DG)(DT)(DG)(DG)(DT)(DG)(DT)(DG)(DT)(DG)(DG)(DT)(DG) GTGGTGTGTGGTG A polydeoxyribonucleotide n n n n n n n n n n n n n 1 1.94 36.7 Large, flat hexagon VAPOR DIFFUSION, HANGING DROP 6.0 0.08 M Strontium chloride, 0.04 M Sodium cacodylate 6.0, 35% w/v MPD, 0.012 M Spermine tetrahydrochloride 285 -3.514 3 6 A 10 A 13 -91.701 A_DG10:DG13_A 1 -4.968 1.610 0.183 3.236 -1.928 3 6 A 11 A 8 89.869 A_DG11:DG8_A 2 -7.056 -1.455 0.108 -3.459 -1.945 3 6 A 1 A 4 -90.543 A_DG1:DG4_A 3 3.794 1.449 -0.002 3.531 -3.299 -65.625 A A 10 11 -0.300 A A 13 8 -3.272 0.325 0.590 1.807 AA_DG10DG11:DG8DG13_AA 1 2.640 2.436 -65.578 -1.654 0.436 -0.021 -179.936 A A 11 1 1.327 A A 8 4 -0.022 -2.654 1.454 3.580 AA_DG11DG1:DG4DG8_AA 2 -5.652 -2.826 -179.936 -1.790 0.727 repository Initial release 1 0 2026-07-22 United States National Institutes of Health/National Cancer Institute (NIH/NCI) 1R15CA253134 lyatsun1@swarthmore.edu 0000-0003-3946-0939 Liliya Yatsunyk principal investigator/group leader N RCSB Y RCSB 2025-07-15 REL REL PGE TRIETHYLENE GLYCOL K POTASSIUM ION SR STRONTIUM ION HOH water 32630 synthetic construct sample 1 13 N N 6FQ2 Intermolecular left-handed G-quadruplex PDB experimental model PGE 102 2 PGE PGE 101 A K 1 3 K K 102 A K 2 3 K K 103 A SR 1 4 SR SR 104 A SR 2 4 SR SR 105 A HOH 1 5 HOH HOH 201 A HOH 4 5 HOH HOH 202 A HOH 5 5 HOH HOH 203 A HOH 7 5 HOH HOH 204 A HOH 10 5 HOH HOH 205 A DG 1 n 1 DG 1 A DT 2 n 2 DT 2 A DG 3 n 3 DG 3 A DG 4 n 4 DG 4 A DT 5 n 5 DT 5 A DG 6 n 6 DG 6 A DT 7 n 7 DT 7 A DG 8 n 8 DG 8 A DT 9 n 9 DT 9 A DG 10 n 10 DG 10 A DG 11 n 11 DG 11 A DT 12 n 12 DT 12 A DG 13 n 13 DG 13 A author_defined_assembly 1 monomeric none A DG 1 A O6 DG 1 1_555 A K 102 C K K 1_555 A DG 3 A O6 DG 3 1_555 93.8 A DG 1 A O6 DG 1 1_555 A K 102 C K K 1_555 A DG 4 A O6 DG 4 1_555 66.8 A DG 3 A O6 DG 3 1_555 A K 102 C K K 1_555 A DG 4 A O6 DG 4 1_555 78.5 A DG 1 A O6 DG 1 1_555 A K 102 C K K 1_555 A DG 6 A O6 DG 6 1_555 154.2 A DG 3 A O6 DG 3 1_555 A K 102 C K K 1_555 A DG 6 A O6 DG 6 1_555 72.9 A DG 4 A O6 DG 4 1_555 A K 102 C K K 1_555 A DG 6 A O6 DG 6 1_555 88.7 A DG 1 A O6 DG 1 1_555 A K 102 C K K 1_555 A DG 8 A O6 DG 8 1_555 102.2 A DG 3 A O6 DG 3 1_555 A K 102 C K K 1_555 A DG 8 A O6 DG 8 1_555 131.4 A DG 4 A O6 DG 4 1_555 A K 102 C K K 1_555 A DG 8 A O6 DG 8 1_555 66.9 A DG 6 A O6 DG 6 1_555 A K 102 C K K 1_555 A DG 8 A O6 DG 8 1_555 73.2 A DG 1 A O6 DG 1 1_555 A K 102 C K K 1_555 A DG 10 A O6 DG 10 1_555 132.3 A DG 3 A O6 DG 3 1_555 A K 102 C K K 1_555 A DG 10 A O6 DG 10 1_555 107.1 A DG 4 A O6 DG 4 1_555 A K 102 C K K 1_555 A DG 10 A O6 DG 10 1_555 158.0 A DG 6 A O6 DG 6 1_555 A K 102 C K K 1_555 A DG 10 A O6 DG 10 1_555 73.3 A DG 8 A O6 DG 8 1_555 A K 102 C K K 1_555 A DG 10 A O6 DG 10 1_555 95.2 A DG 1 A O6 DG 1 1_555 A K 102 C K K 1_555 A DG 11 A O6 DG 11 1_555 68.1 A DG 3 A O6 DG 3 1_555 A K 102 C K K 1_555 A DG 11 A O6 DG 11 1_555 158.3 A DG 4 A O6 DG 4 1_555 A K 102 C K K 1_555 A DG 11 A O6 DG 11 1_555 103.5 A DG 6 A O6 DG 6 1_555 A K 102 C K K 1_555 A DG 11 A O6 DG 11 1_555 128.5 A DG 8 A O6 DG 8 1_555 A K 102 C K K 1_555 A DG 11 A O6 DG 11 1_555 66.8 A DG 10 A O6 DG 10 1_555 A K 102 C K K 1_555 A DG 11 A O6 DG 11 1_555 79.2 A DG 1 A O6 DG 1 1_555 A K 102 C K K 1_555 A DG 13 A O6 DG 13 1_555 76.4 A DG 3 A O6 DG 3 1_555 A K 102 C K K 1_555 A DG 13 A O6 DG 13 1_555 74.1 A DG 4 A O6 DG 4 1_555 A K 102 C K K 1_555 A DG 13 A O6 DG 13 1_555 131.9 A DG 6 A O6 DG 6 1_555 A K 102 C K K 1_555 A DG 13 A O6 DG 13 1_555 118.8 A DG 8 A O6 DG 8 1_555 A K 102 C K K 1_555 A DG 13 A O6 DG 13 1_555 154.2 A DG 10 A O6 DG 10 1_555 A K 102 C K K 1_555 A DG 13 A O6 DG 13 1_555 69.4 A DG 11 A O6 DG 11 1_555 A K 102 C K K 1_555 A DG 13 A O6 DG 13 1_555 89.5 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 1 A O6 DG 1 1_555 0.0 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 4 A O6 DG 4 1_555 64.4 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 4 A O6 DG 4 1_555 64.4 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 4 A O6 DG 4 1_555 64.4 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 4 A O6 DG 4 1_555 64.4 A DG 4 A O6 DG 4 1_555 A K 103 D K K 1_555 A DG 4 A O6 DG 4 1_555 0.0 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 8 A O6 DG 8 1_555 101.0 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 8 A O6 DG 8 1_555 101.0 A DG 4 A O6 DG 4 1_555 A K 103 D K K 1_555 A DG 8 A O6 DG 8 1_555 71.2 A DG 4 A O6 DG 4 1_555 A K 103 D K K 1_555 A DG 8 A O6 DG 8 1_555 71.2 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 8 A O6 DG 8 1_555 101.0 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 8 A O6 DG 8 1_555 101.0 A DG 4 A O6 DG 4 1_555 A K 103 D K K 1_555 A DG 8 A O6 DG 8 1_555 71.2 A DG 4 A O6 DG 4 1_555 A K 103 D K K 1_555 A DG 8 A O6 DG 8 1_555 71.2 A DG 8 A O6 DG 8 1_555 A K 103 D K K 1_555 A DG 8 A O6 DG 8 1_555 0.0 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 63.1 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 63.1 A DG 4 A O6 DG 4 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 102.4 A DG 4 A O6 DG 4 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 102.4 A DG 8 A O6 DG 8 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 67.8 A DG 8 A O6 DG 8 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 67.8 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 63.1 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 63.1 A DG 4 A O6 DG 4 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 102.4 A DG 4 A O6 DG 4 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 102.4 A DG 8 A O6 DG 8 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 67.8 A DG 8 A O6 DG 8 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 67.8 A DG 11 A O6 DG 11 1_555 A K 103 D K K 1_555 A DG 11 A O6 DG 11 1_555 0.0 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 2.21 0.30 108.30 110.51 A A A O4' C1' N9 DG DG DG 6 6 6 N 51.79 0.2042 0.1675 0.1695 1.54 26.75 256 4860 5116 5.00 95.36 0.1557 1 FREE R-VALUE 1.37 MOLECULAR REPLACEMENT 14.5806 0.9000 1.1000 GeoStd + Monomer Library + CDL v1.2 FLAT BULK SOLVENT MODEL 1.54 26.75 5 292 14 273 0 0.0116 324 1.1834 490 0.0535 51 0.0132 13 38.2614 140 0.2980 0.1996 1.93 118 2345 95.13 0.1935 0.1630 26.75 138 2515 95.57 28.21 1.538 57.044 9PLC 5136 0.999 0.074 0.013 0.075 1 18.9 34.4 95.8 2.965 1.538 1.565 1.3 258 0.510 0.485 3.005 1 100.0 refinement PHENIX 1.21.2_5419 data reduction autoPROC data scaling autoPROC phasing PHENIX 1.21.2_5419 179 hexagonal P 65 2 2 P 65 2 (x,y,z+1/12) x,y,z x-y,x,z+5/6 y,-x+y,z+1/6 -y,x-y,z+2/3 -x+y,-x,z+1/3 x-y,-y,-z -x,-x+y,-z+1/3 -x,-y,z+1/2 y,x,-z+2/3 -y,-x,-z+1/6 -x+y,y,-z+1/2 x,x-y,-z+5/6 N JLM3 left-handed, parallel G-quadruplex in P65 2 2 Spacegroup 1 N N 2 N N 3 N N 3 N N 4 N N 4 N N 5 N N metalc 2.759 A DG 1 A O6 DG 1 1_555 A K 102 C K K 1_555 metalc 3.019 A DG 1 A O6 DG 1 1_555 A K 103 D K K 1_555 metalc 2.576 A DG 1 A O6 DG 1 1_555 A K 103 D K K 12_564 metalc 2.862 A DG 3 A O6 DG 3 1_555 A K 102 C K K 1_555 metalc 2.874 A DG 4 A O6 DG 4 1_555 A K 102 C K K 1_555 metalc 2.790 A DG 4 A O6 DG 4 1_555 A K 103 D K K 1_555 metalc 2.971 A DG 4 A O6 DG 4 1_555 A K 103 D K K 12_564 metalc 2.743 A DG 6 A O6 DG 6 1_555 A K 102 C K K 1_555 metalc 2.817 A DG 8 A O6 DG 8 1_555 A K 102 C K K 1_555 metalc 2.594 A DG 8 A O6 DG 8 1_555 A K 103 D K K 1_555 metalc 2.983 A DG 8 A O6 DG 8 1_555 A K 103 D K K 12_564 metalc 2.801 A DG 10 A O6 DG 10 1_555 A K 102 C K K 1_555 metalc 2.792 A DG 11 A O6 DG 11 1_555 A K 102 C K K 1_555 metalc 2.921 A DG 11 A O6 DG 11 1_555 A K 103 D K K 1_555 metalc 2.681 A DG 11 A O6 DG 11 1_555 A K 103 D K K 12_564 metalc 2.754 A DG 13 A O6 DG 13 1_555 A K 102 C K K 1_555 hydrog TYPE_6_PAIR A DG 1 A N1 DG 1 1_555 A DG 4 A O6 DG 4 1_555 hydrog TYPE_6_PAIR A DG 1 A N2 DG 1 1_555 A DG 4 A N7 DG 4 1_555 hydrog TYPE_6_PAIR A DG 1 A N7 DG 1 1_555 A DG 11 A N2 DG 11 1_555 hydrog TYPE_6_PAIR A DG 1 A O6 DG 1 1_555 A DG 11 A N1 DG 11 1_555 hydrog TYPE_6_PAIR A DG 3 A N1 DG 3 1_555 A DG 6 A O6 DG 6 1_555 hydrog TYPE_6_PAIR A DG 3 A N2 DG 3 1_555 A DG 6 A N7 DG 6 1_555 hydrog TYPE_6_PAIR A DG 3 A N7 DG 3 1_555 A DG 13 A N2 DG 13 1_555 hydrog TYPE_6_PAIR A DG 3 A O6 DG 3 1_555 A DG 13 A N1 DG 13 1_555 hydrog TYPE_6_PAIR A DG 4 A N1 DG 4 1_555 A DG 8 A O6 DG 8 1_555 hydrog TYPE_6_PAIR A DG 4 A N2 DG 4 1_555 A DG 8 A N7 DG 8 1_555 hydrog TYPE_6_PAIR A DG 6 A N1 DG 6 1_555 A DG 10 A O6 DG 10 1_555 hydrog TYPE_6_PAIR A DG 6 A N2 DG 6 1_555 A DG 10 A N7 DG 10 1_555 hydrog TYPE_6_PAIR A DG 8 A N1 DG 8 1_555 A DG 11 A O6 DG 11 1_555 hydrog TYPE_6_PAIR A DG 8 A N2 DG 8 1_555 A DG 11 A N7 DG 11 1_555 hydrog TYPE_6_PAIR A DG 10 A N1 DG 10 1_555 A DG 13 A O6 DG 13 1_555 hydrog TYPE_6_PAIR A DG 10 A N2 DG 10 1_555 A DG 13 A N7 DG 13 1_555 DNA G-quadruplex, left-handed G-quadruplex, parallel, bulge, DNA 9PLC PDB 1 1 9PLC 1 13 9PLC 1 13 9PLC A 1 1 13 179 P 65 2 2 P 65 2 (x,y,z+1/12)